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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2021-12-09, 11:50 based on data in: /mnt/raid7/Dachuang/Achuan/PRJNA633959/1-fastqc


        General Statistics

        Showing 342/342 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        SRR11825857_1
        87.6%
        54%
        0.0
        SRR11825857_2
        78.5%
        54%
        0.0
        SRR11825858_1
        90.8%
        53%
        0.1
        SRR11825858_2
        77.7%
        54%
        0.1
        SRR11825859_1
        90.7%
        53%
        0.0
        SRR11825859_2
        77.0%
        53%
        0.0
        SRR11825860_1
        88.5%
        53%
        0.0
        SRR11825860_2
        80.0%
        54%
        0.0
        SRR11825861_1
        91.4%
        55%
        0.1
        SRR11825861_2
        76.8%
        55%
        0.1
        SRR11825862_1
        89.6%
        58%
        0.0
        SRR11825862_2
        76.2%
        57%
        0.0
        SRR11825863_1
        90.0%
        54%
        0.0
        SRR11825863_2
        75.8%
        54%
        0.0
        SRR11825864_1
        87.7%
        53%
        0.0
        SRR11825864_2
        73.0%
        53%
        0.0
        SRR11825865_1
        89.4%
        53%
        0.0
        SRR11825865_2
        81.6%
        53%
        0.0
        SRR11825866_1
        89.1%
        52%
        0.1
        SRR11825866_2
        73.0%
        53%
        0.1
        SRR11825867_1
        92.3%
        55%
        0.0
        SRR11825867_2
        78.8%
        55%
        0.0
        SRR11825868_1
        87.9%
        53%
        0.1
        SRR11825868_2
        73.4%
        53%
        0.1
        SRR11825869_1
        89.0%
        53%
        0.0
        SRR11825869_2
        80.3%
        53%
        0.0
        SRR11825870_1
        89.0%
        55%
        0.1
        SRR11825870_2
        71.9%
        55%
        0.1
        SRR11825871_1
        90.0%
        52%
        0.1
        SRR11825871_2
        76.4%
        53%
        0.1
        SRR11825872_1
        90.0%
        53%
        0.1
        SRR11825872_2
        76.5%
        53%
        0.1
        SRR11825873_1
        86.5%
        55%
        0.0
        SRR11825873_2
        77.0%
        56%
        0.0
        SRR11825874_1
        89.4%
        56%
        0.0
        SRR11825874_2
        79.8%
        55%
        0.0
        SRR11825875_1
        89.8%
        54%
        0.1
        SRR11825875_2
        73.6%
        54%
        0.1
        SRR11825876_1
        93.1%
        54%
        0.1
        SRR11825876_2
        80.7%
        56%
        0.1
        SRR11825877_1
        89.7%
        54%
        0.1
        SRR11825877_2
        76.3%
        54%
        0.1
        SRR11825878_1
        87.1%
        54%
        0.1
        SRR11825878_2
        79.0%
        54%
        0.1
        SRR11825879_1
        89.0%
        53%
        0.1
        SRR11825879_2
        73.5%
        53%
        0.1
        SRR11825880_1
        93.1%
        54%
        0.1
        SRR11825880_2
        81.0%
        55%
        0.1
        SRR11825881_1
        87.5%
        50%
        0.1
        SRR11825881_2
        74.4%
        51%
        0.1
        SRR11825882_1
        90.1%
        54%
        0.1
        SRR11825882_2
        80.6%
        54%
        0.1
        SRR11825883_1
        89.5%
        54%
        0.1
        SRR11825883_2
        73.2%
        54%
        0.1
        SRR11825884_1
        88.8%
        55%
        0.0
        SRR11825884_2
        72.2%
        55%
        0.0
        SRR11825885_1
        89.3%
        52%
        0.1
        SRR11825885_2
        74.8%
        52%
        0.1
        SRR11825886_1
        87.2%
        52%
        0.1
        SRR11825886_2
        73.2%
        53%
        0.1
        SRR11825887_1
        86.9%
        52%
        0.0
        SRR11825887_2
        77.5%
        52%
        0.0
        SRR11825888_1
        92.1%
        53%
        0.1
        SRR11825888_2
        74.5%
        54%
        0.1
        SRR11825889_1
        92.5%
        53%
        0.1
        SRR11825889_2
        80.0%
        54%
        0.1
        SRR11825890_1
        91.0%
        52%
        0.1
        SRR11825890_2
        76.6%
        53%
        0.1
        SRR11825891_1
        89.1%
        53%
        0.0
        SRR11825891_2
        80.4%
        54%
        0.0
        SRR11825892_1
        89.1%
        53%
        0.1
        SRR11825892_2
        73.2%
        53%
        0.1
        SRR11825893_1
        93.5%
        54%
        0.1
        SRR11825893_2
        81.5%
        55%
        0.1
        SRR11825894_1
        88.1%
        53%
        0.1
        SRR11825894_2
        75.0%
        53%
        0.1
        SRR11825895_1
        89.8%
        53%
        0.0
        SRR11825895_2
        74.6%
        53%
        0.0
        SRR11825896_1
        87.7%
        54%
        0.0
        SRR11825896_2
        72.2%
        54%
        0.0
        SRR11825897_1
        84.3%
        55%
        0.0
        SRR11825897_2
        74.5%
        55%
        0.0
        SRR11825898_1
        91.9%
        52%
        0.1
        SRR11825898_2
        78.2%
        53%
        0.1
        SRR11825899_1
        88.1%
        53%
        0.1
        SRR11825899_2
        73.6%
        54%
        0.1
        SRR11825900_1
        89.3%
        57%
        0.0
        SRR11825900_2
        80.2%
        56%
        0.0
        SRR11825901_1
        90.9%
        54%
        0.1
        SRR11825901_2
        75.9%
        55%
        0.1
        SRR11825902_1
        91.0%
        57%
        0.1
        SRR11825902_2
        78.8%
        57%
        0.1
        SRR11825903_1
        89.1%
        54%
        0.1
        SRR11825903_2
        75.1%
        53%
        0.1
        SRR11825904_1
        90.8%
        53%
        0.0
        SRR11825904_2
        82.4%
        53%
        0.0
        SRR11825905_1
        87.4%
        53%
        0.0
        SRR11825905_2
        79.8%
        53%
        0.0
        SRR11825906_1
        91.9%
        57%
        0.1
        SRR11825906_2
        79.0%
        57%
        0.1
        SRR11825907_1
        90.6%
        56%
        0.1
        SRR11825907_2
        76.3%
        57%
        0.1
        SRR11825908_1
        89.0%
        54%
        0.1
        SRR11825908_2
        76.4%
        55%
        0.1
        SRR11825909_1
        87.4%
        55%
        0.1
        SRR11825909_2
        79.5%
        54%
        0.1
        SRR11825910_1
        90.3%
        52%
        0.1
        SRR11825910_2
        79.4%
        53%
        0.1
        SRR11825911_1
        88.4%
        53%
        0.1
        SRR11825911_2
        74.4%
        53%
        0.1
        SRR11825912_1
        87.9%
        55%
        0.0
        SRR11825912_2
        79.3%
        54%
        0.0
        SRR11825913_1
        87.3%
        55%
        0.1
        SRR11825913_2
        70.2%
        56%
        0.1
        SRR11825914_1
        94.7%
        58%
        0.1
        SRR11825914_2
        85.2%
        58%
        0.1
        SRR11825915_1
        89.7%
        53%
        0.1
        SRR11825915_2
        72.8%
        54%
        0.1
        SRR11825916_1
        89.0%
        53%
        0.1
        SRR11825916_2
        74.1%
        53%
        0.1
        SRR11825917_1
        90.5%
        53%
        0.1
        SRR11825917_2
        81.9%
        53%
        0.1
        SRR11825918_1
        88.5%
        52%
        0.1
        SRR11825918_2
        72.1%
        54%
        0.1
        SRR11825919_1
        95.0%
        56%
        0.1
        SRR11825919_2
        84.1%
        57%
        0.1
        SRR11825920_1
        88.3%
        58%
        0.1
        SRR11825920_2
        75.9%
        58%
        0.1
        SRR11825921_1
        89.3%
        56%
        0.1
        SRR11825921_2
        81.3%
        56%
        0.1
        SRR11825922_1
        90.0%
        57%
        0.1
        SRR11825922_2
        75.5%
        57%
        0.1
        SRR11825923_1
        93.0%
        60%
        0.0
        SRR11825923_2
        81.3%
        59%
        0.0
        SRR11825924_1
        87.9%
        58%
        0.0
        SRR11825924_2
        74.3%
        57%
        0.0
        SRR11825925_1
        88.5%
        55%
        0.0
        SRR11825925_2
        78.4%
        55%
        0.0
        SRR11825926_1
        92.1%
        54%
        0.0
        SRR11825926_2
        78.1%
        55%
        0.0
        SRR11825927_1
        91.0%
        56%
        0.0
        SRR11825927_2
        73.1%
        56%
        0.0
        SRR11825928_1
        91.1%
        52%
        0.0
        SRR11825928_2
        77.7%
        53%
        0.0
        SRR11825929_1
        87.7%
        54%
        0.0
        SRR11825929_2
        69.5%
        54%
        0.0
        SRR11825930_1
        86.7%
        57%
        0.0
        SRR11825930_2
        71.1%
        57%
        0.0
        SRR11825931_1
        91.4%
        53%
        0.0
        SRR11825931_2
        76.9%
        53%
        0.0
        SRR11825932_1
        87.9%
        57%
        0.0
        SRR11825932_2
        72.8%
        56%
        0.0
        SRR11825933_1
        87.7%
        53%
        0.0
        SRR11825933_2
        77.9%
        53%
        0.0
        SRR11825934_1
        87.1%
        52%
        0.0
        SRR11825934_2
        68.4%
        53%
        0.0
        SRR11825935_1
        91.6%
        53%
        0.0
        SRR11825935_2
        78.9%
        53%
        0.0
        SRR11825936_1
        90.1%
        56%
        0.0
        SRR11825936_2
        75.4%
        56%
        0.0
        SRR11825937_1
        87.6%
        53%
        0.0
        SRR11825937_2
        77.5%
        53%
        0.0
        SRR11825938_1
        89.4%
        53%
        0.0
        SRR11825938_2
        72.3%
        54%
        0.0
        SRR11825939_1
        90.2%
        55%
        0.0
        SRR11825939_2
        75.7%
        55%
        0.0
        SRR11825940_1
        91.2%
        56%
        0.0
        SRR11825940_2
        77.9%
        55%
        0.0
        SRR11825941_1
        90.5%
        55%
        0.0
        SRR11825941_2
        80.9%
        54%
        0.0
        SRR11825942_1
        90.3%
        55%
        0.0
        SRR11825942_2
        81.5%
        53%
        0.0
        SRR11825943_1
        89.7%
        53%
        0.1
        SRR11825943_2
        72.8%
        53%
        0.1
        SRR11825944_1
        89.7%
        53%
        0.1
        SRR11825944_2
        75.8%
        53%
        0.1
        SRR11825945_1
        90.4%
        54%
        0.0
        SRR11825945_2
        77.3%
        54%
        0.0
        SRR11825946_1
        85.7%
        54%
        0.0
        SRR11825946_2
        77.5%
        53%
        0.0
        SRR11825947_1
        86.5%
        56%
        0.1
        SRR11825947_2
        69.4%
        56%
        0.1
        SRR11825948_1
        91.8%
        55%
        0.1
        SRR11825948_2
        79.2%
        54%
        0.1
        SRR11825949_1
        89.8%
        54%
        0.0
        SRR11825949_2
        75.5%
        53%
        0.0
        SRR11825950_1
        89.5%
        52%
        0.0
        SRR11825950_2
        80.9%
        53%
        0.0
        SRR11825951_1
        89.5%
        57%
        0.1
        SRR11825951_2
        73.8%
        56%
        0.1
        SRR11825952_1
        88.6%
        59%
        0.0
        SRR11825952_2
        71.3%
        59%
        0.0
        SRR11825953_1
        90.2%
        53%
        0.1
        SRR11825953_2
        77.2%
        53%
        0.1
        SRR11825954_1
        91.4%
        55%
        0.0
        SRR11825954_2
        78.9%
        56%
        0.0
        SRR11825955_1
        87.5%
        52%
        0.0
        SRR11825955_2
        78.7%
        52%
        0.0
        SRR11825956_1
        90.4%
        54%
        0.1
        SRR11825956_2
        74.8%
        54%
        0.1
        SRR11825957_1
        91.6%
        53%
        0.1
        SRR11825957_2
        78.3%
        53%
        0.1
        SRR11825958_1
        88.6%
        53%
        0.1
        SRR11825958_2
        75.0%
        53%
        0.1
        SRR11825959_1
        91.1%
        52%
        0.1
        SRR11825959_2
        82.4%
        53%
        0.1
        SRR11825960_1
        90.2%
        54%
        0.1
        SRR11825960_2
        74.3%
        55%
        0.1
        SRR11825961_1
        90.0%
        52%
        0.1
        SRR11825961_2
        75.5%
        53%
        0.1
        SRR11825962_1
        86.4%
        52%
        0.0
        SRR11825962_2
        69.3%
        53%
        0.0
        SRR11825963_1
        89.7%
        55%
        0.0
        SRR11825963_2
        75.7%
        55%
        0.0
        SRR11825964_1
        91.1%
        55%
        0.0
        SRR11825964_2
        82.8%
        56%
        0.0
        SRR11825965_1
        88.1%
        53%
        0.1
        SRR11825965_2
        70.5%
        54%
        0.1
        SRR11825966_1
        90.3%
        53%
        0.1
        SRR11825966_2
        76.6%
        53%
        0.1
        SRR11825967_1
        85.7%
        53%
        0.0
        SRR11825967_2
        69.9%
        53%
        0.0
        SRR11825968_1
        87.4%
        52%
        0.0
        SRR11825968_2
        77.7%
        52%
        0.0
        SRR11825969_1
        93.7%
        54%
        0.1
        SRR11825969_2
        79.1%
        56%
        0.1
        SRR11825970_1
        87.8%
        50%
        0.1
        SRR11825970_2
        71.8%
        51%
        0.1
        SRR11825971_1
        90.8%
        53%
        0.1
        SRR11825971_2
        78.3%
        54%
        0.1
        SRR11825972_1
        87.9%
        54%
        0.0
        SRR11825972_2
        74.4%
        54%
        0.0
        SRR11825973_1
        87.6%
        58%
        0.1
        SRR11825973_2
        79.8%
        58%
        0.1
        SRR11825974_1
        92.9%
        59%
        0.1
        SRR11825974_2
        80.6%
        58%
        0.1
        SRR11825975_1
        91.4%
        53%
        0.1
        SRR11825975_2
        78.9%
        55%
        0.1
        SRR11825976_1
        88.6%
        52%
        0.1
        SRR11825976_2
        76.1%
        54%
        0.1
        SRR11825977_1
        88.9%
        53%
        0.1
        SRR11825977_2
        80.4%
        53%
        0.1
        SRR11825978_1
        89.7%
        54%
        0.1
        SRR11825978_2
        75.4%
        54%
        0.1
        SRR11825979_1
        87.3%
        54%
        0.0
        SRR11825979_2
        69.9%
        54%
        0.0
        SRR11825980_1
        91.9%
        55%
        0.1
        SRR11825980_2
        79.5%
        56%
        0.1
        SRR11825981_1
        90.9%
        54%
        0.1
        SRR11825981_2
        78.8%
        55%
        0.1
        SRR11825982_1
        86.4%
        53%
        0.0
        SRR11825982_2
        78.1%
        54%
        0.0
        SRR11825983_1
        89.8%
        56%
        0.1
        SRR11825983_2
        75.5%
        56%
        0.1
        SRR11825984_1
        91.2%
        54%
        0.1
        SRR11825984_2
        78.5%
        55%
        0.1
        SRR11825985_1
        89.1%
        54%
        0.1
        SRR11825985_2
        75.1%
        55%
        0.1
        SRR11825986_1
        89.7%
        57%
        0.1
        SRR11825986_2
        80.8%
        57%
        0.1
        SRR11825987_1
        89.6%
        54%
        0.1
        SRR11825987_2
        74.5%
        53%
        0.1
        SRR11825988_1
        93.3%
        54%
        0.1
        SRR11825988_2
        80.9%
        54%
        0.1
        SRR11825989_1
        89.4%
        56%
        0.1
        SRR11825989_2
        77.2%
        56%
        0.1
        SRR11825990_1
        89.3%
        53%
        0.0
        SRR11825990_2
        75.4%
        54%
        0.0
        SRR11825991_1
        90.3%
        56%
        0.1
        SRR11825991_2
        82.2%
        56%
        0.1
        SRR11825992_1
        91.1%
        56%
        0.1
        SRR11825992_2
        75.7%
        56%
        0.1
        SRR11825993_1
        89.4%
        54%
        0.1
        SRR11825993_2
        77.1%
        54%
        0.1
        SRR11825994_1
        87.8%
        50%
        0.1
        SRR11825994_2
        75.5%
        51%
        0.1
        SRR11825995_1
        88.9%
        57%
        0.1
        SRR11825995_2
        80.7%
        56%
        0.1
        SRR11825996_1
        87.3%
        52%
        0.1
        SRR11825996_2
        74.1%
        54%
        0.1
        SRR11825997_1
        91.0%
        56%
        0.0
        SRR11825997_2
        79.1%
        56%
        0.0
        SRR11825998_1
        90.6%
        55%
        0.0
        SRR11825998_2
        77.9%
        55%
        0.0
        SRR11825999_1
        87.7%
        58%
        0.0
        SRR11825999_2
        79.1%
        57%
        0.0
        SRR11826000_1
        88.7%
        53%
        0.1
        SRR11826000_2
        71.1%
        53%
        0.1
        SRR11826001_1
        87.1%
        54%
        0.0
        SRR11826001_2
        70.7%
        54%
        0.0
        SRR11826002_1
        91.4%
        52%
        0.0
        SRR11826002_2
        81.2%
        53%
        0.0
        SRR11826003_1
        90.9%
        55%
        0.0
        SRR11826003_2
        77.5%
        56%
        0.0
        SRR11826004_1
        85.9%
        53%
        0.0
        SRR11826004_2
        78.0%
        54%
        0.0
        SRR11826005_1
        88.4%
        53%
        0.1
        SRR11826005_2
        78.6%
        54%
        0.1
        SRR11826006_1
        86.8%
        53%
        0.1
        SRR11826006_2
        70.2%
        54%
        0.1
        SRR11826007_1
        89.7%
        56%
        0.1
        SRR11826007_2
        72.5%
        55%
        0.1
        SRR11826008_1
        92.0%
        53%
        0.1
        SRR11826008_2
        78.0%
        54%
        0.1
        SRR11826009_1
        87.8%
        53%
        0.1
        SRR11826009_2
        72.5%
        53%
        0.1
        SRR11826010_1
        89.3%
        56%
        0.1
        SRR11826010_2
        80.8%
        55%
        0.1
        SRR11826011_1
        92.0%
        56%
        0.1
        SRR11826011_2
        75.7%
        56%
        0.1
        SRR11826012_1
        91.6%
        56%
        0.1
        SRR11826012_2
        78.0%
        56%
        0.1
        SRR11826013_1
        90.0%
        57%
        0.1
        SRR11826013_2
        75.9%
        56%
        0.1
        SRR11826014_1
        85.6%
        54%
        0.1
        SRR11826014_2
        76.7%
        54%
        0.1
        SRR11826015_1
        89.0%
        54%
        0.1
        SRR11826015_2
        71.8%
        54%
        0.1
        SRR11826016_1
        87.2%
        52%
        0.0
        SRR11826016_2
        70.4%
        52%
        0.0
        SRR11826017_1
        89.0%
        52%
        0.1
        SRR11826017_2
        75.4%
        52%
        0.1
        SRR11826018_1
        89.1%
        51%
        0.1
        SRR11826018_2
        73.7%
        52%
        0.1
        SRR11826019_1
        89.6%
        56%
        0.1
        SRR11826019_2
        80.2%
        54%
        0.1
        SRR11826020_1
        86.4%
        50%
        0.1
        SRR11826020_2
        70.0%
        51%
        0.1
        SRR11826021_1
        92.8%
        54%
        0.0
        SRR11826021_2
        82.2%
        55%
        0.0
        SRR11826022_1
        89.1%
        61%
        0.1
        SRR11826022_2
        77.2%
        61%
        0.1
        SRR11826023_1
        86.6%
        52%
        0.0
        SRR11826023_2
        78.2%
        53%
        0.0
        SRR11826024_1
        88.7%
        54%
        0.1
        SRR11826024_2
        73.5%
        54%
        0.1
        SRR11826025_1
        92.4%
        56%
        0.0
        SRR11826025_2
        79.6%
        56%
        0.0
        SRR11826026_1
        86.5%
        51%
        0.0
        SRR11826026_2
        73.4%
        51%
        0.0
        SRR11826027_1
        87.4%
        53%
        0.0
        SRR11826027_2
        77.1%
        53%
        0.0

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge..

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        All samples have sequences of a single length (295bp , 296bp , 297bp , 298bp , 299bp , 301bp). See the General Statistics Table.

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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